Optics collection and detection system and method

Abstract

Optics collection and detection systems are provided for measuring optical signals from an array of optical sources over time. Methods of using the optics collection and detection systems are also described.

What is claimed is: 
     
       1. An integrated device for measuring optical signals from an array of optical sources over time, the device comprising a chip comprising:
 a top layer comprising an array of nanoscale apertures, each nanoscale aperture forming a nanoscale well for receiving a fluid sample material, to form the array of optical sources wherein an optical source in the array of optical sources emits two or more optical signals, each optical signal comprising different wavelengths, and at least one optical signal comprising a signal emitted from a chemical or biochemical reaction in the sample material; 
 a middle layer comprising an array of spectral diversion elements corresponding to the array of optical sources; and 
 a bottom layer comprising a detector sensitive to spatial distributions of light; 
 wherein each corresponding spectral diversion element in the array of spectral diversion elements diverts each of the two or more optical signals of a respective optical source in the array of optical sources onto a different region of the bottom layer, whereby identities of the optical signals can be identified by relative spatial light intensities across the detector, and 
 wherein the top layer, the middle layer and the bottom layer are integrated and wherein the optical signals emitted from the sample material in the top layer are diverted to the bottom layer without passing through air or free space. 
 
     
     
       2. The integrated device of  claim 1  wherein the optical source comprises a zero mode waveguide and the optical signals are emitted from fluorescent labels corresponding to a chemical or biochemical reaction occurring within the zero mode waveguide. 
     
     
       3. The integrated device of  claim 2  wherein the chemical or biochemical reaction comprises nucleic acid synthesis. 
     
     
       4. The integrated device of  claim 1  wherein the spectral diversion element comprises an optical grating or holographic element. 
     
     
       5. The integrated device of  claim 1  wherein the spectral diversion element comprises a Bragg grating disposed at an angle to the normal to the central ray of the emitted light. 
     
     
       6. The integrated device of  claim 1  wherein the detector includes multiple proximal pixels and wherein the pixels are in a linear array. 
     
     
       7. The integrated device of  claim 1  wherein the detector includes multiple proximal pixels and wherein the pixels are in a two dimensional array. 
     
     
       8. The integrated device of  claim 1  wherein four different optical signals are emitted from each optical source. 
     
     
       9. The integrated device of  claim 8  wherein corresponding to each optical source, the detector has four pixels, each pixel corresponding to one of the four optical signals whereby the spectral diversion element diverts each of the four different optical signals to a different pixel in the four pixels. 
     
     
       10. The integrated device of  claim 1  wherein the spectral diversion element comprises a lens. 
     
     
       11. The integrated device of  claim 10  wherein the lens is cylindrically symmetrical and diverts different wavelengths of light at different angles from the center of the lens resulting in a circularly symmetric pattern on the detector for each set of wavelengths. 
     
     
       12. The integrated device of  claim 11  wherein corresponding to each optical source, the detector comprises one central pixel and one or more pixels comprising a circular ring around the central pixel. 
     
     
       13. An integrated device for measuring optical signals from an array of optical sources over time, the device comprising a chip comprising:
 a top layer comprising an array of nanoscale apertures, each nanoscale aperture forming a nanoscale well for receiving a fluid sample material, to form the array of optical sources wherein an optical source in the array of optical sources emits two or more optical signals, each optical signal having a different rate of signal decay; 
 a middle layer transmitting light from the top layer to a bottom layer; and 
 the bottom layer comprising a detector having a pixel array; 
 wherein the top layer, the middle layer and the bottom layer are integrated and wherein the optical signals emitted from the optical sources in the top layer are transmitted to the bottom layer without passing through air or free space, and 
 wherein a single pixel in the pixel array measures the characteristic absorption depth of each of the two or more optical signals, allowing the pixel to distinguish the identity of each of the optical signals. 
 
     
     
       14. An integrated device for measuring optical signals from an array of optical sources over time, the device comprising:
 a top layer comprising the array of optical sources wherein an optical source in the array of optical sources comprises a sample material and emits two or more optical signals, each optical signal comprising different wavelengths, and at least one optical signal comprising a signal emitted from a chemical or biochemical reaction in the sample material; 
 a middle layer comprising an array of spectral diversion elements, wherein a spectral diversion element in the array of spectral diversion elements comprising a PBG stack having two or more photon band gap (PBG) elements, each PBG element configured to allow light of a different transmission wavelength range through the element and to reflect light that is not in the transmission wavelength range; and 
 a bottom layer comprising a detector; 
 wherein each PBG element transmits light onto a different detection region of the detector, whereby the identity of the optical signal can be identified by the regions of the detector onto which light is transmitted.